HAS3

hyaluronan synthase 3, the group of Glycosyltransferase family 2

Basic information

Region (hg38): 16:69105652-69118719

Links

ENSG00000103044 ∙ NCBI:3038 ∙ OMIM:602428 ∙ HGNC:4820 ∙ Uniprot:O00219 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HAS3 gene.

• Inborn genetic diseases (16 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAS3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			16		2	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	3

Variants in HAS3

This is a list of pathogenic ClinVar variants found in the HAS3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-69109424-G-A		not specified	Uncertain significance (Mar 27, 2023)
16-69109487-C-T		not specified	Uncertain significance (Feb 15, 2023)
16-69109508-C-T		not specified	Uncertain significance (Nov 29, 2023)
16-69109531-G-A		not specified	Uncertain significance (Jan 26, 2022)
16-69109536-G-T			Uncertain significance (-)
16-69109579-T-C		not specified	Uncertain significance (Aug 22, 2023)
16-69109597-C-T			Uncertain significance (-)
16-69109609-C-T			Benign (Sep 05, 2018)
16-69109712-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-69109825-G-A		not specified	Uncertain significance (Dec 05, 2022)
16-69109850-G-A		not specified	Uncertain significance (Aug 02, 2023)
16-69109883-C-T		not specified	Uncertain significance (Jan 24, 2023)
16-69109909-G-A		not specified	Uncertain significance (May 24, 2023)
16-69109912-C-T		not specified	Uncertain significance (Sep 20, 2023)
16-69109919-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-69113465-G-C		not specified	Uncertain significance (Sep 13, 2023)
16-69114389-G-A		not specified	Uncertain significance (Jan 20, 2023)
16-69114484-C-T		not specified	Uncertain significance (Jan 08, 2024)
16-69114848-C-T		not specified	Uncertain significance (Jan 03, 2022)
16-69114950-G-A		not specified	Uncertain significance (Dec 20, 2021)
16-69115002-G-C		not specified	Uncertain significance (Oct 04, 2022)
16-69115181-C-G			Benign (Dec 31, 2019)
16-69115194-A-G			Benign (Dec 31, 2019)
16-69115261-G-C		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAS3	protein_coding	protein_coding	ENST00000306560	3	13156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.883	0.117	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	218	353	0.617	0.0000235	3565
Missense in Polyphen		39	104.03	0.3749		1036
Synonymous	-1.42	175	153	1.15	0.0000104	1159
Loss of Function	3.85	4	24.6	0.163	0.00000156	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the addition of GlcNAc or GlcUA monosaccharides to the nascent hyaluronan polymer. Therefore, it is essential to hyaluronan synthesis a major component of most extracellular matrices that has a structural role in tissues architectures and regulates cell adhesion, migration and differentiation. This is one of the isozymes catalyzing that reaction (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.86

Haploinsufficiency Scores

• pHI: 0.664
• hipred: Y
• hipred_score: 0.714
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.803

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Has3
• Phenotype: respiratory system phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;hyaluronan biosynthetic process;extracellular polysaccharide biosynthetic process;positive regulation of transcription, DNA-templated;extracellular matrix assembly;positive regulation of hyaluranon cable assembly
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane;integral component of membrane;hyaluranon cable
• Molecular function: protein binding;identical protein binding;hyaluronan synthase activity